Six hours after Jamal Mirsaidov met with the British ambassador, the limp and mutilated corpse of his grandson was dumped on his doorstep. The body was battered and one arm appeared to have been immersed in boiling fluid until the skin had begun to peel off. Mirsaidov is a literature professor in the ancient city of Samarkand. His mistake had been to write a letter to Tony Blair and George Bush alerting them to the daily torture meted out to dissidents in Uzbekistan, their new ally in the war on terror.

Mirsaidov and the ambassador, Craig Murray, doubt the letter was ever delivered but Murray ensured his message was. And though the local prosecutor concluded that the 18-year-old had died of a drug overdose, Murray is convinced he paid the ultimate price for his grandfather's dissent. "The professor has no doubt at all that his grandson was murdered in response to my visit. I wrestle with my conscience greatly over whether I caused that boy's horrible death."

Murray has paid a more direct price for his decision to step out of the bubble of isolation and immunity in which most diplomats live and challenge such abuses. His distinctly undiplomatic assessment of Uzbekistan's human rights record propelled him into a lengthy battle with the Foreign Office. He was subjected to a humiliating disciplinary investigation, had his personal life publicly shredded and suffered a string of health problems. He became the rogue ambassador. Not so much Our Man in Tashkent as Our Uzbekistan Problem.

Last weekend, in an exclusive interview with the Guardian and Channel 4 News, he spoke for the first time about his turbulent year. "I had a period under psychiatric care as an in-patient for depression last autumn. I've gone through the break-up of my marriage. In November, I suffered a pulmonary embolism and very nearly died. It is most unlikely that I will be an ambassador again after I leave [my post here], I think for the very reason you are interviewing me now. An aura of controversy is not one that is useful to the diplomatic corps."

Twelve months ago Murray was a British ambassador in a place few people had heard of, with an eccentric collection of Wallace and Gromit and Dennis the Menace ties, and some unconventional views. He had arrived in Tashkent - at 43 one of Britain's youngest ambassadors - after a distinguished spell in Africa where he helped expose the Sandline affair and broker a peace deal in Sierra Leone. He had turned down three honours from the Queen for his work, considering letters after his name "not his thing". He liked a drink in some of the capital's vibrant - and sometimes lascivious - bars, but it was his attitude to the Uzbekistan regime's slim grasp of human rights that marked him out from fellow diplomats.

Murray was determined not to let the regime's abuses be drowned out by the country's newfound strategic importance. Uzbekistan had allowed the Pentagon to hire a vital military base in the southern town of Kharshi to aid the hunt for Osama bin Laden in neighbouring Afghanistan. In return, Tashkent got about half a billion dollars in aid a year. Some of the aid itself highlighted American double standards. In 2002, $79 million went to the Uzbekistani security forces and law enforcement (in 2002, the US aid budget to Uzbekistan was $220 million in total) - the same people whom the State Department accused of "using torture as a routine investigation technique".

Murray has plenty of first-hand evidence of the Uzbekistani's "routine methods". Sitting in the plush living room of his ambassadorial residence, he tells me: "People come to me very often after being tortured. Normally this includes homosexual and heterosexual rape of close relatives in front of the victim; rape with objects such as broken bottles; asphyxiation; pulling out of fingernails; smashing of limbs with blunt objects; and use of boiling liquids including complete immersion of the body. This is not uncommon. Thousands of people a year suffer from this torture at the hands of the authorities."

As Murray saw apparently innocent Muslims being sentenced to death after confessions extracted by torture and show trials, he became furious at the "conspiracy of silence" practised by his fellow diplomats. "I tried to find out whether anyone had made a policy decision to [say nothing]", he says. "But certainly within the British government no minister had ever said such a thing. I was determined to blow the lid on [the conspiracy of silence]."

In October 2002, Murray made a speech to his fellow diplomats and Uzbekistani officials at a human rights conference in Tashkent in which he became the first western official for four years to state publicly that "Uzbekistan is not a functioning democracy", and to highlight the "prevalence of torture in Uzbekistani prisons" in a system where "brutality is inherent". Highlighting a case in which two men were boiled to death, he added: "All of us know that this is not an isolated incident."

The Foreign Office cleared the speech, but not without an acrimonious struggle over its content. During the dispute he panned one of his superiors in the FCO's eastern department, for questioning whether the number of political prisoners in Uzbekistan had increased. According to a British official familiar with the correspondence, he wrote: "I understand that you might find this fact politically inconvenient. If you wish me to omit it, then say so. But don't pretend it isn't true." He attacked his superior for his "sadly cautious and above all completely unimaginative" censures, and attacked the "classic public school and Oxbridge influenced FCO house style", as "ponderous, self-important and ineffective".

The speech began to take on a life of its own. Kofi Annan raised its contents during a meeting with Uzbekistani president Islam Karimov. It became a serious thorn in Tashkent's - and Washington's - side. Murray's confrontational style pressed it further into the flesh. In the build-up to the Iraq war, he could not contain his fury at the "double standards" being practised by Washington. He wrote to his superiors in London on the day in which he watched Bush talk of "dismantling the apparatus of terror" and "removing the torture and rape rooms" in Iraq, pointing out that "when it comes to the Karimov regime, systematic torture and rape appear to be treated as peccadilloes, not to effect the relationship and to be downplayed in the international fora ... I hope that once the present crisis is over we will make plain to the US, at senior level, our serious concern over their policy in Uzbekistan."

The email got him called back to London for a carpeting on March 8. In that same tense month, his personal life became more complicated when he met Nadira Alieva, an attractive, 23-year-old English teacher with a passion for the dancefloor, in a Tashkent bar. They soon began an affair.

Over the coming months, another, quite unrelated, drama unfolded in the embassy. Chris Hirst, the embassy's third secretary, was accused by the local authorities of attacking local Uzbekistanis on the capital's streets often accompanied by his baseball bat and rottweiler. The authorities had been pushed into making formal complaints against Hirst. While he was out of town, a complaint got through to Murray and he had him immediately sent back to London. Subsequently Hirst resigned.

Life quietened down over the next few months until Murray was about to go on holiday in July. While the ambassador was in the FCO's King Charles Street headquarters, en route to Canada, one of his locally hired staff rang to say she and several others had been fired on orders from London. Murray stormed around the FCO, outraged, and they were reinstated before he flew out.

Yet three weeks into his break, he received an email from London calling him back. On August 21, he sat in an office as the personnel department outlined 18 disciplinary charges. Most were not supported by any evidence and others were petty. He was accused of "hiring dolly birds for above the usual rate" to work in the visa department, which had, he insists, an all-male staff. Yet he was also accused of having sex in his office with local girls in exchange for visas to the UK. The FCO said he had a week in which to resign. He was not allowed to discuss the charges with anyone or he would face prosecution - and maybe jail - under the Official Secrets Act. Bemused by where these accusations had come from, he slowly began to unravel at the Kafka-esque ultimatum before him.

On September 2 he had a breakdown, collapsing while having a medical check in Tashkent. He was flown back to London and put on suicide watch in St Thomas's hospital. He told friends he had lost the use of his muscles. He said he felt powerful people were concocting allegations against him and he was not even allowed to call witnesses to defend himself. Murray refused to resign, and the pressure continued. In September, the FCO sent out a senior official, Tony Crombie, who was instructed to interview only staff in the Tashkent embassy as part of an investigation into the charges. Some staff dismissed the charges as nonsense, while others provided meagre support for claims that Murray had at times appeared a little "worse for wear" in the mornings.

Crombie returned to London saying there was no case to answer over 16 of the 18 charges. Crombie said there was information that might require two of the charges to be investigated - that he was "drunk at work" and had misused the embassy Range Rover.

Murray was allowed to return to Tashkent after extensive health checks, and the Foreign Office continued to deny there was any investigation. Yet once he arrived home after his six-hour business-class flight, he began to feel severe back pains. Forty-eight hours later, he was air ambulanced out of Tashkent with a serious pulmonary embolism in his lung. Again he found himself in St Thomas's Hospital, having narrowly escaped death.

In January, once his health was restored, Murray was officially exonerated by the Foreign Office. Yet was told he was guilty of telling other people about the case, and got a written warning. "It was basically a warning saying, 'Step out of line again and you will be sacked,'" says a source who saw it.

But Murray's troubles were not over yet. In February, the Mail on Sunday revealed his relationship with Alieva. Fiona, his wife, who friends say was aware of the affair, could not stomach the public humiliation and left Tashkent. She is now separated from Murray, and has taken his 10-year-old daughter, Emily, with her back to London.

Today, Murray lives alone, bar visits from Alieva, in a small but palatial residence in Tashkent. His many bedrooms are empty and his pool largely unused - Murray can't swim. The crackle of his guards' walkie-talkies occasionally interrupts the polite trickle of the garden's water feature.

It is a lonely end to a once promising, if unexpected, career. "I had always wanted to be a whisky salesman," says Murray. Yet, in 1984, he sat the civil service entrance exams, which he passed with flying colours. In Africa, he befriended Kofi Annan, and the state-school educated, Dundee University graduate, rose rapidly in the Foreign Office.

Twenty years later, his disillusionment is complete, the Foreign Office having refused his request to stay on another year, and asking him to leave Tashkent in November 2005 as scheduled. He believes a paper-shuffling job in the bowels of King Charles Street awaits. "I think obviously on a purely human level," he says, "if something like this happens to anyone inside an organisation that you've worked in for 20 years, you're never going to feel the same trust."

Murray is in no doubt, friends say, that the FCO investigation was aimed at discrediting him because of the unwanted attention his public comments was bringing to Uzbekistani human-rights abuses. Recipients of US aid have to have their human-rights record vetted by the State Department before they can receive funding. Murray's comments were highlighting medieval abuses the US wanted to turn a blind eye to. Things have changed since Murray's first poked his head above the diplomatic parapet: on Tuesday the US State Department declared that Uzbekistan's human rights record meant it could no longer be certified as fit to receive aid.

Murray says he has begun to fear for his own safety. He says he would like bullet-proof glass for his home's windows, but the FCO has yet to find the funds for this. At the same time, he receives regular security warnings from London about specific threats to his life. "I'm not thinking a sniper is going to get us at any minute," he says, "but in this part of the world there is nowhere you are safe from threats." Asked to respond to this article, the FCO declined to comment on the personal circumstances of its staff, or security matters.

Nevertheless his work - a sort of diplomatic outreach service - goes on, driven by what Murray calls "a deep personal commitment". He has turned down a lucrative human rights job in New York because he does not want to desert people who he believes rely on his presence for protection. One of them is Alieva, who was rounded up by the police in the days after a series of bombings and shootings in March which were blamed on al-Qaida. Her alleged involvement in the blasts seems laughable, given she is a 23-year-old with a greater affinity to Beyoncé than Bin Laden. Yet she claims the police beat her and threatened to rape her, trying to extort money for her release. Alieva says she was spared only by a phonecall to Murray. "She was on crutches for a fortnight," Murray says. "I am just glad I managed to get there before anything worse could have happened. Her safety is one of my biggest worries."

Murray describes the Uzbekistan regime as "kleptocratic". Tashkent has begun shutting down private businesses, ensuring all economic activity - from the cotton picked by child labour to the gold mines - lines the presidential elite's pockets. The borders have been closed. Import duty is at 70%. In a bid to suppress inflation and prevent businesses growing, the government has stopped printing money, made it illegal to buy things with dollars, and limited the amount of the local currency in circulation. British American Tobacco, the largest foreign employer in the country, cannot find enough sums to pay its staff and is apparently considering withdrawing from the country.

The refuge for survivors of self-immolation in Samarkand testifies to the extremes of despair Uzbekistan's poverty inspires. It provides emergency burns treatments and a place to hide while the wounds heal. Most of its 130 clients last year were women subjected to domestic violence and rape, often at the hands of their new in-laws. Others were escapees or deportees from the slave trade to Russia, the Middle East and South East Asia. I accompany Murray as he hands the director $1,000 in British Embassy cash as an FCO donation to keep the shelter running. "It's very hard to imagine being so desperate to want to kill yourself in that way," he says. "For these women it's the end of the world, and there is nothing left for them."

The FCO insists Murray represents its point of view, yet is remarkably nervous about this interview, contacting Murray and myself several times on the day before we meet. Its concern is understandable: Murray is not discreet. As he himself admits: "There is no point in having cocktail-party relationships with a fascist regime." He says he advocates a new style of ambassadorship, one that is more down to earth and less stuffy. "You don't have to be a pompous old fart to be an ambassador."

Yet this lack of discretion also applies to his personal life. Murray's great sin, in the eyes of the FCO, may be that he chose to live the life of a typical expat in the former Soviet Union. He is an unashamed socialiser, almost keen to let me know that he cares little how much I see of his colourful personal life. On Friday night, he takes me to the Rande-vue bar beneath one of Samarkand's hotels. We begin in the Bohar restaurant, where a series of dancing girls in traditional costume, then in cowboy outfits, parade on stage, while Murray drinks a couple of neat whiskies. Then we move on to the Jazz Bar in the Meridian hotel, where workers for Halliburton, servicing the US base at Kharshi come to unwind in the company of local girls. "I joined the Foreign Office, not a monastery," Murray explains. "I have no intention of living like a monk - not that I have anything against monks. It has been put to me that this is perhaps not what ambassadors do..."

At the Foreign Office there are some who feel Murray should have drawn a line under his battle with London, quietly returning to work, stiff upper lip intact. One FCO official suggested in his correspondence with Murray, that the ambassador should have just called the abuses "horrid", sat down, and then toed the line. Murray replied: "As you may know I have a slight speech impediment and cannot call anything 'howwid'."

· You can see Nick Paton Walsh's exclusive TV report on Craig Murray tonight on Channel 4 news at 7pm